Sodium in PDB 5jg1: Hiv-1 Wild Type Protease with Grl-031-14A (A Adamantane P1-Ligand with Tetrahydropyrano-Tetrahydrofuran in P2 and Isobutylamine in P1')

The structure of Hiv-1 Wild Type Protease with Grl-031-14A (A Adamantane P1-Ligand with Tetrahydropyrano-Tetrahydrofuran in P2 and Isobutylamine in P1'), PDB code: 5jg1 was solved by Y.-F.Wang, J.Agniswamy, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.16
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.040, 86.406, 45.987, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 19.2

The structure of Hiv-1 Wild Type Protease with Grl-031-14A (A Adamantane P1-Ligand with Tetrahydropyrano-Tetrahydrofuran in P2 and Isobutylamine in P1') also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Hiv-1 Wild Type Protease with Grl-031-14A (A Adamantane P1-Ligand with Tetrahydropyrano-Tetrahydrofuran in P2 and Isobutylamine in P1') (pdb code 5jg1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Hiv-1 Wild Type Protease with Grl-031-14A (A Adamantane P1-Ligand with Tetrahydropyrano-Tetrahydrofuran in P2 and Isobutylamine in P1'), PDB code: 5jg1:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Hiv-1 Wild Type Protease with Grl-031-14A (A Adamantane P1-Ligand with Tetrahydropyrano-Tetrahydrofuran in P2 and Isobutylamine in P1')


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hiv-1 Wild Type Protease with Grl-031-14A (A Adamantane P1-Ligand with Tetrahydropyrano-Tetrahydrofuran in P2 and Isobutylamine in P1') within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:16.9 occ:1.00 O A:HOH637 2.3 16.2 1.0 O A:ASP60 2.4 12.7 1.0 O A:HOH618 2.4 15.9 1.0 O A:HOH638 2.4 29.3 1.0 O A:HOH635 2.5 22.8 1.0 O A:HOH664 2.6 22.4 1.0 C A:ASP60 3.4 11.2 1.0 N A:ASP60 3.8 11.3 1.0 CA A:ASP60 4.1 11.2 1.0 O A:ARG41 4.1 14.3 1.0 CB A:ASP60 4.4 12.9 1.0 CB A:GLN61 4.4 14.6 1.0 N A:GLN61 4.5 12.2 1.0 N A:ARG41 4.5 18.5 1.0 O A:HOH659 4.6 21.4 0.5 O A:GLN61 4.6 16.1 1.0 CD1 A:ILE62 4.7 16.6 1.0 C A:TYR59 4.7 9.8 1.0 O A:PRO39 4.7 17.6 1.0 CA A:GLN61 4.8 12.5 1.0 C A:GLN61 4.8 11.7 1.0 CA A:GLY40 4.8 19.1 1.0

Sodium binding site 2 out of 3 in the Hiv-1 Wild Type Protease with Grl-031-14A (A Adamantane P1-Ligand with Tetrahydropyrano-Tetrahydrofuran in P2 and Isobutylamine in P1')


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Hiv-1 Wild Type Protease with Grl-031-14A (A Adamantane P1-Ligand with Tetrahydropyrano-Tetrahydrofuran in P2 and Isobutylamine in P1') within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:25.4 occ:1.00 O B:HOH345 2.3 19.2 1.0 O B:HOH370 2.4 39.4 1.0 O B:ASP60 2.5 12.3 1.0 O B:HOH325 2.7 24.6 1.0 C B:ASP60 3.5 11.2 1.0 N B:ASP60 3.7 10.9 1.0 O B:HOH374 3.9 29.7 1.0 CA B:ASP60 4.0 11.4 1.0 O B:ARG41 4.2 13.0 1.0 CB B:ASP60 4.3 12.0 1.0 N B:GLN61 4.6 10.6 1.0 C B:TYR59 4.6 9.0 1.0 O B:PRO39 4.6 13.8 1.0 CD1 B:ILE62 4.7 11.6 1.0 CB B:GLN61 4.7 12.5 1.0 O B:GLN61 4.9 15.0 1.0 CA B:GLN61 4.9 10.9 1.0 CA B:TYR59 5.0 8.7 1.0 C B:GLN61 5.0 10.7 1.0 N B:ARG41 5.0 10.9 1.0

Sodium binding site 3 out of 3 in the Hiv-1 Wild Type Protease with Grl-031-14A (A Adamantane P1-Ligand with Tetrahydropyrano-Tetrahydrofuran in P2 and Isobutylamine in P1')


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Hiv-1 Wild Type Protease with Grl-031-14A (A Adamantane P1-Ligand with Tetrahydropyrano-Tetrahydrofuran in P2 and Isobutylamine in P1') within 5.0Å range: probe atom residue distance (Å) B Occ B:Na203 b:27.3 occ:1.00 O B:HOH341 2.1 31.4 1.0 O B:HOH389 2.3 30.4 0.5 O B:HOH329 2.3 19.9 0.5 O B:HOH326 2.4 27.1 1.0 O B:HOH404 2.6 29.7 0.5 O B:HOH310 2.8 15.4 1.0 OH B:TYR59 3.9 13.2 1.0 CA B:SER37 4.1 16.9 0.3 CA B:SER37 4.1 17.1 0.7 O B:LEU38 4.3 14.0 1.0 NH2 B:ARG57 4.3 17.7 1.0 OG B:SER37 4.3 26.2 0.3 N B:LEU38 4.3 13.4 1.0 O B:HOH304 4.3 15.1 1.0 CB B:SER37 4.4 19.9 0.3 OG B:SER37 4.4 21.1 0.7 CB B:SER37 4.5 20.2 0.7 O B:MET36 4.6 14.7 1.0 C B:SER37 4.8 14.8 1.0 O B:HOH335 4.9 26.4 0.5 CZ B:TYR59 4.9 11.1 1.0

A.K.Ghosh, H.L.Osswald, K.Glauninger, J.Agniswamy, Y.F.Wang, H.Hayashi, M.Aoki, I.T.Weber, H.Mitsuya. Probing Lipophilic Adamantyl Group As the P1-Ligand For Hiv-1 Protease Inhibitors: Design, Synthesis, Protein X-Ray Structural Studies, and Biological Evaluation. J.Med.Chem. V. 59 6826 2016.
ISSN: ISSN 0022-2623
PubMed: 27389367
DOI: 10.1021/ACS.JMEDCHEM.6B00639